chr1:161643798:T>C Detail (hg19) (FCGR2B)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr1:161,643,798-161,643,798
hg38	chr1:161,674,008-161,674,008 View the variant detail on this assembly version.

HGVS

FCGR2B

Type	Transcript	Protein
RefSeq	NM_001002273.2:c.695T>C	NP_001002273.1:p.Ile232Thr
	NM_001002274.2:c.695T>C	NP_001002274.1:p.Ile232Thr
	NM_001190828.1:c.674T>C	NP_001177757.1:p.Ile225Thr
	NM_001002275.2:c.695T>C	NP_001002275.1:p.Ile232Thr
	NM_004001.4:c.695T>C	NP_003992.3:p.Ile232Thr
Ensemble	ENST00000236937.13:c.695T>C	ENST00000236937.13:p.Ile232Thr
	ENST00000367961.8:c.674T>C	ENST00000367961.8:p.Ile225Thr
	ENST00000358671.10:c.695T>C	ENST00000358671.10:p.Ile232Thr

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.206
	ToMMo:0.243
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.341

Prediction

ClinVar

Clinical Significance	protective; risk factor
Review star
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Links

FCGR2B

Type	Database	ID	Link
Gene	MIM	604590	OMIM
	HGNC	3618	HGNC
	Ensembl	ENSG00000072694	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv3532724	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
risk factor	2010-04-27	no assertion criteria provided	Systemic lupus erythematosus, susceptibility to	germline	Detail
protective	2015-05-18	no assertion criteria provided	Malaria, resistance to	germline	Detail

CIViC

Disease	Drug	EL	ET	ED	CS	VO	TR	Pubmed	Links
breast cancer		B	Prognostic	Supports	Poor Outcome	Common Germline	4	24989892	Detail

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.247	Lupus Erythematosus, Systemic	A single nucleotide polymorphism in human FcγRIIB (rs1050501) results in profoun...	BeFree	25022320	Detail
<0.001	HIV Infections	We found for the first time associations between cryptococcal meningitis and FCG...	BeFree	22879986	Detail
<0.001	Meningitis, Cryptococcal	We found for the first time associations between cryptococcal meningitis and FCG...	BeFree	22879986	Detail
<0.001	Central Nervous System Infection	We found for the first time associations between cryptococcal meningitis and FCG...	BeFree	22879986	Detail
0.006	rheumatoid arthritis	This study was performed to examine whether FCGR2B-I232T was associated with sus...	BeFree	12486608	Detail
<0.001	asthma	Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18...	BeFree	24586589	Detail
0.003	asthma	Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18...	BeFree	24586589	Detail
0.120	Malaria, resistance to	NA	CLINVAR		Detail
0.247	Lupus Erythematosus, Systemic	In humans, a SLE-associated polymorphism (rs1050501) results in a dysfunctional ...	BeFree	25475856	Detail
0.247	Lupus Erythematosus, Systemic	In FCGR2B encoding an inhibitory receptor expressed in B cells, monocytes and de...	BeFree	17305544	Detail
0.003	asthma	Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18...	BeFree	24586589	Detail

Annotation

Annotations

Descrption	Source	Links
1325 HER2-positive breast cancer patients treated with trastuzumab and chemotherapy from the N9831 c...	CIViC Evidence	Detail
NM_001394477.1(FCGR2B):c.695T>C (p.Ile232Thr) AND Systemic lupus erythematosus, susceptibility to	ClinVar	Detail
NM_001394477.1(FCGR2B):c.695T>C (p.Ile232Thr) AND Malaria, resistance to	ClinVar	Detail
A single nucleotide polymorphism in human FcγRIIB (rs1050501) results in profound receptor dysfuncti...	DisGeNET	Detail
We found for the first time associations between cryptococcal meningitis and FCGR2B 232I/T genotypes...	DisGeNET	Detail
We found for the first time associations between cryptococcal meningitis and FCGR2B 232I/T genotypes...	DisGeNET	Detail
We found for the first time associations between cryptococcal meningitis and FCGR2B 232I/T genotypes...	DisGeNET	Detail
This study was performed to examine whether FCGR2B-I232T was associated with susceptibility to rheum...	DisGeNET	Detail
Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505...	DisGeNET	Detail
Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505...	DisGeNET	Detail
NA	DisGeNET	Detail
In humans, a SLE-associated polymorphism (rs1050501) results in a dysfunctional FcγRIIB(T232) recept...	DisGeNET	Detail
In FCGR2B encoding an inhibitory receptor expressed in B cells, monocytes and dendritic cells, a pol...	DisGeNET	Detail
Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505...	DisGeNET	Detail

Overlapped Transcript Coordinates

Gene	Transcript ID	Exon Number	Chromosome	Start	Stop	Type	Amino Mutation	Transcript Position	Links

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs1050501 dbSNP
Genome: hg19
Position: chr1:161,643,798-161,643,798
Variant Type: snv
Reference Allele: T
Alternative Allele: C
Filtering Status (HGVD): PASS
Filtering Status (HGVD): VQSRTrancheSNP99.00to99.90
# of samples (HGVD): 693
Mean of sample read depth (HGVD): 21.50
Standard deviation of sample read depth (HGVD): 49.77
Number of reference allele (HGVD): 1101
Number of alternative allele (HGVD): 285
Allele Frequency (HGVD): 0.20562770562770563
Gene Symbol (HGVD): FCGR2B
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): VQSRTrancheSNP99.80to99.90
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): rs1050501
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2433
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 4054
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16662
East Asian Chromosome Counts (ExAC): 496
East Asian Allele Counts (ExAC): 169
East Asian Heterozygous Counts (ExAC): 125
East Asian Homozygous Counts (ExAC): 22
East Asian Allele Frequency (ExAC): 0.3407258064516129
Chromosome Counts in All Race (ExAC): 5404
Allele Counts in All Race (ExAC): 1280
Heterozygous Counts in All Race (ExAC): 1024
Homozygous Counts in All Race (ExAC): 128
Allele Frequency in All Race (ExAC): 0.23686158401184307
Variant (CIViC) (CIViC Variant): I232T
Transcript 1 (CIViC Variant): ENST00000358671.5
Variant URL (CIViC Variant): https://civic.genome.wustl.edu/links/variants/458

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